[BioC] Differential anlaysis (limma)

[Wei Shi]

Hi Mohamed:

    I think you can try two things:

(1) Try alternative normalization methods;
(2) Remove probes which are not expressing in all your arrays.

    Hope this helps.

Cheers,
Wei

Mohamed lajnef wrote:
> Dear All,
>
> I'am using limma package to extract the genes diffrentially expressed by 3
> treatment,my database includes
>
> 48803 genes (rows) and 120 colones (40 replicates per treatment),my program
> is as follows:
>
> donne<-exprs(BSData.quantile)
> groups<-as.factor(c(rep("Tem",40),rep("EarlyO",40),rep("LateO",40)))
> design<-model.matrix(~0+groups)
> colnames(design)=levels(groups)
> fit<-lmFit(donne,design)
> cont.matrix<-makeContrasts(TemvsEarlyO=Tem-EarlyO,TemvsLateO=Tem-LateO,EarlyOvsLateO=EarlyO-LateO,
> levels=design)
> fit2<-contrasts.fit(fit, cont.matrix)
> ebfit<-eBayes(fit2)
> gene1<-topTable(ebfit, coef=1)
> gene2<-topTable(ebfit, coef=2)
> gene3<-topTable(ebfit, coef=3)
>
> results<-decideTests(ebfit) # I have a matrix that contains only 0 because
>
> in the ligne 26  results <- new("TestResults", sign(tstat) * (p < p.value))
> of decideTests program  the condition (p<p.value) is always false in my
> case!!
> something is wrong in my program, but I dont know where??
>
> Any help would be appreciated.
>
> Regards
>
> 	[[alternative HTML version deleted]]
>
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